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51. Trends in molecular diagnosis and diversity studies for phytosanitary regulated Xanthomonas

Author

Catara, Vittoria, Cubero, Jaime, Pothier, Joël F., Bosis, Eran, Bragard, Claude, Đermić, Edyta, Holeva, Maria C., Jacques, Marie-Agnès, Petter, Francoise, Pruvost, Olivier, Robène, Isabelle, Studholme, David J., Tavares, Fernando, Vicente, Joana G., Koebnik, Ralf, Costa, Joana, Università degli Studi di Catania, Agencia Estatal de Investigación (España), European Commission, University of Zurich, Scottish Government, Catara, Vittoria, Cubero, Jaime, Pothier, Joël F., Bosis, Eran, Bragard, Claude, Đermić, Edyta, Holeva, Maria C., Jacques, Marie-Agnès, Petter, Francoise, Pruvost, Olivier, Robène, Isabelle, Studholme, David J., Tavares, Fernando, Vicente, Joana G., Koebnik, Ralf, Costa, Joana, University of Catania [Italy], Department of Agriculture, Food and Environment, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Zürich University of Applied Sciences (ZHAW), ORT Braude College [Karmiel, Israel], Earth and Life Institute [Louvain-La-Neuve] (ELI), Université Catholique de Louvain = Catholic University of Louvain (UCL), Faculty of Agriculture [Zagreb] (UNIZG), University of Zagreb, Benaki Phytopathological Institute, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), European and Mediterranean Plant Protection Organization - Organisation Européenne et Méditerranéenne pour la Protection des Plantes (EPPO), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), University of Exeter, Biosciences, College of Life and Environmental Sciences, Faculdade de Ciências da Universidade do Porto (FCUP), Universidade do Porto, Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO), Fera Science Ltd, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), University of Coimbra [Portugal] (UC), Centre for Functional Ecology, Instituto Pedro Nunes (IPN), J.C. (Joana Costa) acknowledges R&D Unit Center for Functional Ecology-Science for People and the Planet (CFE), with reference UIDB/04004/2020, financed by FCT/MCTES through national funds (PIDDAC). V.C. acknowledges support of the University of Catania PIA.CE.RI. 2020–2022Linea 2-Research Project MEDIT-ECO. J.C. acknowledges support from AEI by RTI 2018-096018-R-C31 and FEDER. O.P. and I.R. acknowledge the European Union (ERDF, EAFRD) and Réunion regional council for support. J.F.P. acknowledges support from the Department of Life Sciences and Facility Management of the Zurich University of Applied Sciences (ZHAW) in Wädenswil. D.J.S. and J.G.V. also acknowledge joint funding by a grant from BBSRC, NERC, Defra, and the Scottish Government, under the Strategic Priorities Fund Plant Bacterial Diseases programme under the project ‘Xanthomonas plants diseases: mitigating existing, emerging and future threats to UK agriculture’ (BB/T010916/1 and BB/T010908/1). The APC was funded by COST (European Cooperation inScience and technology)., Benaki Phytopathological Institute (BPI), Université d'Angers (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Universidade do Porto = University of Porto, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Centre for Functional ecology, and UCL - SST/ELI/ELIM - Applied Microbiology

Subjects
Xanthomonas, QH301-705.5, Review, molecular methods, Maladie des plantes, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Diagnostic, Biology (General), H20 - Maladies des plantes, Regulated non-quarantine pests, 572: Biochemie, Biotechnologie végétale, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Maladie bactérienne, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, quarantine pests, Molecular methods, Quarantine pests, 579: Mikrobiologie, Mesure phytosanitaire, regulated non-quarantine pests
Abstract

30 Pág. Departamento de ​Protección Vegetal (INIA), Bacteria in the genus Xanthomonas infect a wide range of crops and wild plants, with most species responsible for plant diseases that have a global economic and environmental impact on the seed, plant, and food trade. Infections by Xanthomonas spp. cause a wide variety of non-specific symptoms, making their identification difficult. The coexistence of phylogenetically close strains, but drastically different in their phenotype, poses an added challenge to diagnosis. Data on future climate change scenarios predict an increase in the severity of epidemics and a geographical expansion of pathogens, increasing pressure on plant health services. In this context, the effectiveness of integrated disease management strategies strongly depends on the availability of rapid, sensitive, and specific diagnostic methods. The accumulation of genomic information in recent years has facilitated the identification of new DNA markers, a cornerstone for the development of more sensitive and specific methods. Nevertheless, the challenges that the taxonomic complexity of this genus represents in terms of diagnosis together with the fact that within the same bacterial species, groups of strains may interact with distinct host species demonstrate that there is still a long way to go. In this review, we describe and discuss the current molecular-based methods for the diagnosis and detection of regulated Xanthomonas, taxonomic and diversity studies in Xanthomonas and genomic approaches for molecular diagnosis., J.C. (Joana Costa) acknowledges R&D Unit Center for Functional Ecology-Science for People and the Planet (CFE), with reference UIDB/04004/2020, financed by FCT/MCTES through national funds (PIDDAC). V.C. acknowledges support of the University of Catania PIA.CE.RI. 2020–2022 Linea 2-Research Project MEDIT-ECO. J.C. acknowledges support from AEI by RTI2018-096018-R-C31 and FEDER. O.P. and I.R. acknowledge the European Union (ERDF, EAFRD) and Réunion regional council for support. J.F.P. acknowledges support from the Department of Life Sciences and Facility Management of the Zurich University of Applied Sciences (ZHAW) in Wädenswil. D.J.S. and J.G.V. also acknowledge joint funding by a grant from BBSRC, NERC, Defra, and the Scottish Government, under the Strategic Priorities Fund Plant Bacterial Diseases programme under the project ‘Xanthomonas plants diseases: mitigating existing, emerging and future threats to UK agriculture’ (BB/T010916/1 and BB/T010908/1). The APC was funded by COST (European Cooperation in Science and technology).

Published
2021

58. Molecular epidemiology of Xanthomonas euvesicatoria strains from the Balkan Peninsula revealed by a new multiple-locus variable-number tandem-repeat analysis scheme

Author

Vancheva, Taca, Bogatzevska, Nevena, Moncheva, Penka, Mitrev, Sasa, Vernière, Christian, Koebnik, Ralf, Vancheva, Taca, Bogatzevska, Nevena, Moncheva, Penka, Mitrev, Sasa, Vernière, Christian, and Koebnik, Ralf

Abstract

Bacterial spot of pepper and tomato is caused by at least three species of Xanthomonas, among them two pathovars of Xanthomonas euvesicatoria, which are responsible for significant yield losses on all continents. In order to trace back the spread of bacterial spot pathogens within and among countries, we developed the first multilocus variable number of tandem repeat analyses (MLVA) scheme for pepper- and tomato-pathogenic strains of X. euvesicatoria. In this work, we assessed the repeat numbers by DNA sequencing of 16 tandem repeat loci and applied this new tool to analyse a representative set of 88 X. euvesicatoria pepper strains from Bulgaria and North Macedonia. The MLVA-16 scheme resulted in a Hunter–Gaston Discriminatory Index (HGDI) score of 0.944 and allowed to resolve 36 MLVA haplotypes (MTs), thus demonstrating its suitability for high-resolution molecular typing. Strains from the different regions of Bulgaria and North Macedonia were found to be widespread in genetically distant clonal complexes or singletons. Sequence types of the variable number of tandem repeats (VNTR) amplicons revealed cases of size homoplasy and suggested the coexistence of different populations and different introduction events. The large geographical distribution of MTs and the existence of epidemiologically closely related strains in different regions and countries suggest long dispersal of strains on pepper in this area.

Published
2021

60. Trends in Molecular Diagnosis and Diversity Studies for Phytosanitary Regulated Xanthomonas

Author

UCL - SST/ELI/ELIM - Applied Microbiology, Catara, Vittoria, Cubero, Jaime, Pothier, Joël F., Bosis, Eran, Bragard, Claude, Đermić, Edyta, Holeva, Maria C., Jacques, Marie-Agnès, Petter, Francoise, Pruvost, Olivier, Robène, Isabelle, Studholme, David J., Tavares, Fernando, Vicente, Joana G., Koebnik, Ralf, Costa, Joana, UCL - SST/ELI/ELIM - Applied Microbiology, Catara, Vittoria, Cubero, Jaime, Pothier, Joël F., Bosis, Eran, Bragard, Claude, Đermić, Edyta, Holeva, Maria C., Jacques, Marie-Agnès, Petter, Francoise, Pruvost, Olivier, Robène, Isabelle, Studholme, David J., Tavares, Fernando, Vicente, Joana G., Koebnik, Ralf, and Costa, Joana

Abstract

Bacteria in the genus Xanthomonas infect a wide range of crops and wild plants, with most species responsible for plant diseases that have a global economic and environmental impact on the seed, plant, and food trade. Infections by Xanthomonas spp. cause a wide variety of non-specific symptoms, making their identification difficult. The coexistence of phylogenetically close strains, but drastically different in their phenotype, poses an added challenge to diagnosis. Data on future climate change scenarios predict an increase in the severity of epidemics and a geographical expansion of pathogens, increasing pressure on plant health services. In this context, the effectiveness of integrated disease management strategies strongly depends on the availability of rapid, sensitive, and specific diagnostic methods. The accumulation of genomic information in recent years has facilitated the identification of new DNA markers, a cornerstone for the development of more sensitive and specific methods. Nevertheless, the challenges that the taxonomic complexity of this genus represents in terms of diagnosis together with the fact that within the same bacterial species, groups of strains may interact with distinct host species demonstrate that there is still a long way to go. In this review, we describe and discuss the current molecular-based methods for the diagnosis and detection of regulated Xanthomonas, taxonomic and diversity studies in Xanthomonas and genomic approaches for molecular diagnosis.

Published
2021

61. The Complete Genome Sequence of Xanthomonas theicola, the Causal Agent of Canker on Tea Plants, Reveals Novel Secretion Systems in Clade-1 Xanthomonads

Author

UCL - SST/ELI/ELIM - Applied Microbiology, Koebnik, Ralf, Burokiene, Daiva, Bragard, Claude, Chang, Christine, Saux, Marion Fischer-Le, Kölliker, Roland, Lang, Jillian M., Leach, Jan E., Luna, Emily K., Portier, Perrine, Sagia, Angeliki, Ziegle, Janet, Cohen, Stephen P., Jacobs, Jonathan M., UCL - SST/ELI/ELIM - Applied Microbiology, Koebnik, Ralf, Burokiene, Daiva, Bragard, Claude, Chang, Christine, Saux, Marion Fischer-Le, Kölliker, Roland, Lang, Jillian M., Leach, Jan E., Luna, Emily K., Portier, Perrine, Sagia, Angeliki, Ziegle, Janet, Cohen, Stephen P., and Jacobs, Jonathan M.

Abstract

Xanthomonas theicola is the causal agent of bacterial canker on tea plants. There is no complete genome sequence available for X. theicola, a close relative of the species X. translucens and X. hyacinthi, thus limiting basic research for this group of pathogens. Here, we release a high-quality complete genome sequence for the X. theicola type strain, CFBP 4691T. Single-molecule real-time sequencing with a mean coverage of 264× revealed two contigs of 4,744,641 bp (chromosome) and 40,955 bp (plasmid) in size. Genome mining revealed the presence of nonribosomal peptide synthases, two CRISPR systems, the Xps type 2 secretion system, and the Hrp type 3 secretion system. Surprisingly, this strain encodes an additional type 2 secretion system and a novel type 3 secretion system with enigmatic function, hitherto undescribed for xanthomonads. Four type 3 effector genes were found on complete or partial transposons, suggesting a role of transposons in effector gene evolution and spread. This genome sequence fills an important gap to better understand the biology and evolution of the early-branching xanthomonads, also known as clade-1 xanthomonads.

Published
2021

62. Repeated gain and loss of a single gene modulates the evolution of vascular plant pathogen lifestyles

Author

Emile, Gluck-Thaler, Cerruti, A., Pérez-Quintero, Alvaro L., Veronica, Roman-Reyna, Vishnu, Madhavan, Deepak, Shantharaj, Marcus, Merfa, Taca, Vancheva, Beckham, Gregg T, de La Fuente, Leonardo, Hitendra, Patel, Sonti, Ramesh V., Leach, Jan E., Noël, Laurent D., Slot, Jason C., Jacobs, Jonathan M., Gluck-Thaler, Emile, Cerutti, Aude, Perez-Quintero, Alvaro, Butchacas, Jules, Roman-Reyna, Verónica, Madhavan, Vishnu, Shantharaj, Deepak, Merfa, Marcus, Pesce, Céline, Jauneau, Alain, Vancheva, Taca, Lang, Jillian, Allen, Caitilyn, Verdier, Valerie, Gagnevin, Lionel, Szurek, Boris, Beckham, Gregg, De, Leonardo, Fuente, La, Patel, Hitendra, Sonti, Ramesh, Bragard, Claude, Leach, Jan, Noël, Laurent, Slot, Jason, Koebnik, Ralf, Jacobs, Jonathan, Ohio State University [Columbus] (OSU), University of Pennsylvania, Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Colorado State University [Fort Collins] (CSU), Council of Scientific and Industrial Research [India] (CSIR), Auburn University (AU), Université Catholique de Louvain = Catholic University of Louvain (UCL), National Renewable Energy Laboratory (NREL), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), HM CLAUSE [USA Canada], Plateforme Imagerie [Castanet-Tolosan] (IFR 3450 - Pôle de Biotechnologie Végétale), Institut Fédératif de Recherche, Colorado State University [Pueblo] (CSUPueblo), University of Wisconsin-Madison, UMR - Interactions Plantes Microorganismes Environnement (UMR IPME), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud]), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), NSF Postdoctoral Fellowship in Biology : 1306196, U.S. Fulbright Scholar Award, Science and Engineering Research Board, Government of India : SB/52/JCB-12/2014, European Cooperation in Science and Technology (COST) : CA16107 EuroXanth, United States Department of Energy (DOE) : DE-AC36-08GO28308, United States Department of Energy (DOE), USDA NIFA Postdoctoral Fellowship : 2017-67012-26116, COST SUSTAIN travel grant, National Science Foundation (NSF) : DEB-1638999, Fonds de Recherche du Quebec-Nature et Technologies Doctoral Research Scholarship, University Grants Commission, India, Department of Science & Technology (India), French Ministry of National Education and Research, USDA NIFA through NSF/NIFA Plant Biotic Interactions Program : 2018-67013-28490, ANR-18-CE20-0020,NEPHRON,Analyse génétique et moléculaire de l'immunité de l'hydathode et du système vasculaire(2018), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), University of Pennsylvania [Philadelphia], Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS)

Subjects
0106 biological sciences, Genetics, 0303 health sciences, Xanthomonas, Multidisciplinary, Bacteria, Phylogenetic tree, Hydrolases, Host (biology), Mutagenesis (molecular biology technique), [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Plants, Biology, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, 01 natural sciences, Genome, Phenotype, Pathogenesis, 03 medical and health sciences, Pathogen, Phylogeny, 030304 developmental biology, 010606 plant biology & botany
Abstract

Vascular plant pathogens travel long distances through host veins, leading to life-threatening, systemic infections. In contrast, nonvascular pathogens remain restricted to infection sites, triggering localized symptom development. The contrasting features of vascular and nonvascular diseases suggest distinct etiologies, but the basis for each remains unclear. Here, we show that the hydrolase CbsA acts as a phenotypic switch between vascular and nonvascular plant pathogenesis. cbsA was enriched in genomes of vascular phytopathogenic bacteria in the family Xanthomonadaceae and absent in most nonvascular species. CbsA expression allowed nonvascular Xanthomonas to cause vascular blight, while cbsA mutagenesis resulted in reduction of vascular or enhanced nonvascular symptom development. Phylogenetic hypothesis testing further revealed that cbsA was lost in multiple nonvascular lineages and more recently gained by some vascular subgroups, suggesting that vascular pathogenesis is ancestral. Our results overall demonstrate how the gain and loss of single loci can facilitate the evolution of complex ecological traits. evolution of complex ecological traits.

Published
2020

63. Membrane topology of conserved components of the type III secretion system from the plant pathogen Xanthomonas campestris pv. vesicatoria

Author

Berger, Carolin, Robin, Guillaume P., Bonas, Ulla, and Koebnik, Ralf

Subjects
Beta galactosidases -- Physiological aspects, Beta galactosidases -- Research, Bacteria, Phytopathogenic -- Physiological aspects, Bacteria, Phytopathogenic -- Research, Bacterial proteins -- Physiological aspects, Bacterial proteins -- Research, Biological sciences
Abstract

Type III secretion (T3S) systems play key roles in the assembly of flagella and the translocation of bacterial effector proteins into eukaryotic host cells. Eleven proteins which are conserved among Gram-negative plant and animal pathogenic bacteria have been proposed to build up the basal structure of the T3S system, which spans both inner and outer bacterial membranes. We studied six conserved proteins, termed Hrc, predicted to reside in the inner membrane of the plant pathogen Xanthomonas campestris pv. vesicatoria. The membrane topology of HrcD, HrcR, HrcS, HrcT, HrcU and HrcV was studied by translational fusions to a dual alkaline phosphatase--[beta]-galactosidase reporter protein. Two proteins, HrcU and HrcV, were found to have the same membrane topology as the Yersinia homologues YscU and YscV. For HrcR, the membrane topology differed from the model for the homologue from Yersinia, YscR. For our data on three other protein families, exemplified by HrcD, HrcS and HrcT, we derived the first topology models. Our results provide what is believed to be the first complete model of the inner membrane topology of any bacterial T3S system and will aid in elucidating the architecture of T3S systems by ultrastructural analysis. DOI 10.1099/mic.0.039248-0

Published
2010

64. The Complete Genome Sequence of Xanthomonas theicola, the Causal Agent of Canker on Tea Plants, Reveals Novel Secretion Systems in Clade-1 Xanthomonads

Author

Koebnik, Ralf, primary, Burokiene, Daiva, additional, Bragard, Claude, additional, Chang, Christine, additional, Saux, Marion Fischer-Le, additional, Kölliker, Roland, additional, Lang, Jillian M., additional, Leach, Jan E., additional, Luna, Emily K., additional, Portier, Perrine, additional, Sagia, Angeliki, additional, Ziegle, Janet, additional, Cohen, Stephen P., additional, and Jacobs, Jonathan M., additional

Published
2021
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65. An atypical class of non-coding small RNAs produced in rice leaves upon bacterial infection

Author

Reshetnyak, Ganna, primary, Jacobs, Jonathan M., additional, Auguy, Florence, additional, Sciallano, Coline, additional, Claude, Lisa, additional, Medina, Clemence, additional, Perez-Quintero, Alvaro L., additional, Comte, Aurore, additional, Thomas, Emilie, additional, Bogdanove, Adam, additional, Koebnik, Ralf, additional, Szurek, Boris, additional, Dievart, Anne, additional, Brugidou, Christophe, additional, Lacombe, Severine, additional, and Cunnac, Sebastien, additional

Published
2021
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67. Phylogenetic distribution and evolutionary dynamics of nod and T3SS genes in the genus Bradyrhizobium

Author

Teulet, Albin, Gully, Djamel, Rouy, Zoe, Camuel, Alicia, Koebnik, Ralf, Giraud, Eric, Lassalle, Florent, Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Analyse Bio-Informatique pour la Génomique et le Métabolisme (LABGeM), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), UMR - Interactions Plantes Microorganismes Environnement (UMR IPME), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud]), Imperial College London, Wellcome Trust Genome Campus, French Ministry of National Education, Higher Education and Research, Medical Research Council UK (MRC) MR/N010760/1, ANR-16-CE20-0013,SymEffectors,Système de sécrétion de type 3 pour la symbiose fixatrice d'azote(2016), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), and Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, Genomics, legume, biochemical phenomena, metabolism, and nutrition, symbiosis, type III secretion system, Evolution, Molecular, rhizobium, effector, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Bacterial Proteins, Multigene Family, Type III Secretion Systems, bacteria, nodulation, Bradyrhizobium, Microbe-Niche Interactions: Mutualism, commensalism and parasitism, Phylogeny, Research Article, Peptide Hydrolases
Abstract

International audience; Bradyrhizobium are abundant soil bacteria and the major symbiont of legumes. The recent availability of Bradyrhizobium genome sequences provides a large source of information for analysis of symbiotic traits. In this study, we investigated the evolutionary dynamics of the nodulation genes (nod) and their relationship with the genes encoding type III secretion systems (T3SS) and their effectors among bradyrhizobia. Based on the comparative analysis of 146 Bradyrhizobium genome sequences, we identified six different types of T3SS gene clusters. The two predominant cluster types are designated RhcIa and RhcIb and both belong to the RhcI-T3SS family previously described in other rhizobia. They are found in 92/146 strains, most of them also containing nod genes. RhcIa and RhcIb gene clusters differ in the genes they carry: while the translocon-encoding gene nopX is systematically found in strains containing RhcIb, the nopE and nopH genes are specifically conserved in strains containing RhcIa, suggesting that these last two genes might functionally substitute nopX and play a role related to effector translocation. Phylogenetic analysis suggests that bradyrhizobia simultaneously gained nod and RhcI-T3SS gene clusters via horizontal transfer or subsequent vertical inheritance of a symbiotic island containing both. Sequence similarity searches for known Nop effector proteins in bradyrhizobial proteomes revealed the absence of a so-called core effectome, i.e. that no effector is conserved among all Bradyrhizobium strains. However, NopM and SUMO proteases were found to be the main effector families, being represented in the majority of the genus. This study indicates that bradyrhizobial T3SSs might play a more significant symbiotic role than previously thought and provides new candidates among T3SS structural proteins and effectors for future functional investigations.

Published
2020

68. The Rice DNA-Binding Protein ZBED Controls Stress Regulators and Maintains Disease Resistance After a Mild Drought

Author

Zuluaga, Paola A., Bidzinski, Przemyslaw, Chanclud, Emilie, Ducasse, Aurélie, Cayrol, Bastien, Gomez Selvaraj, Michael, Ishitani, Manabu, Jauneau, Alain, Deslandes, Laurent, Kroj, Thomas, Michel, Corinne, Szurek, Boris, Koebnik, Ralf, Morel, Jean-Benoit, Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), International Center for Tropical Agriculture [Colombie] (CIAT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), UMR - Interactions Plantes Microorganismes Environnement (UMR IPME), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud]), INRA project from the SPE division (Decoy), Agropolis Foundation : 1201-001, Fondazione Cariplo : 1201-001, ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014), Erist, Montpellier, Agricultural Sciences for sustainable Development - - AGRO2010 - ANR-10-LABX-0001 - LABX - VALID, AgreenSkills+ - AGREENSKILLSPLUS - - EC:FP7:PEOPLE2014-05-05 - 2019-05-04 - 609398 - VALID, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), and Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)

Subjects
disease resistance, plant-pathogen interactions, [SDV]Life Sciences [q-bio], drought resistance, fungi, plant– pathogen interactions, food and beverages, Magnaporthe oryzae, Plant Science, lcsh:Plant culture, [SDV] Life Sciences [q-bio], lcsh:SB1-1110, Zn-finger BED domains, plant–pathogen interactions, Original Research
Abstract

BGPI : Equipe 4 : Interactions Céréales Agents Pathogènes (ICAP) ; Equipe 2 : Interactions Virus Insecte Plante (VIP); Background: Identifying new sources of disease resistance and the corresponding underlying resistance mechanisms remains very challenging, particularly in Monocots. Moreover, the modification of most disease resistance pathways made so far is detrimental to tolerance to abiotic stresses such as drought. This is largely due to negative cross-talks between disease resistance and abiotic stress tolerance signaling pathways. We have previously described the role of the rice ZBED protein containing three Zn-finger BED domains in disease resistance against the fungal pathogen Magnaporthe oryzae. The molecular and biological functions of such BED domains in plant proteins remain elusive.Results: Using Nicotiana benthamiana as a heterologous system, we show that ZBED localizes in the nucleus, binds DNA, and triggers basal immunity. These activities require conserved cysteine residues of the Zn-finger BED domains that are involved in DNA binding. Interestingly, ZBED overexpressor rice lines show increased drought tolerance. More importantly, the disease resistance response conferred by ZBED is not compromised by drought-induced stress.Conclusions: Together our data indicate that ZBED might represent a new type of transcriptional regulator playing simultaneously a positive role in both disease resistance and drought tolerance. We demonstrate that it is possible to provide disease resistance and drought resistance simultaneously.

Published
2020
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69. Design of a new multiplex PCR assay for rice pathogenic bacteria detection and its application to infer disease incidence and detect co-infection in rice fields in Burkina Faso

Author

Bangratz, Martine, Wonni, Issa, Kini, Kossi, Sondo, Moussa, Brugidou, Christophe, Béna, Gilles, Gnacko, Fatoumata, Barro, Mariam, Koebnik, Ralf, Silué, Drissa, Tollenaere, Charlotte, UMR - Interactions Plantes Microorganismes Environnement (UMR IPME), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut de l'Environnement et Recherches Agricoles [Ouagadougou] (INERA), Centre national de la recherche scientifique et technologique [Ouagadougou] (CNRST), Africa Rice Center [Côte d'Ivoire] (AfricaRice), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), and ANR-16-IDEX-0006,MUSE,MUSE(2016)

Subjects
DNA, Bacterial, Leaves, Xanthomonas, Burkholderia, Epidemiology, Science, [SDV]Life Sciences [q-bio], Plant Pathogens, Artificial Gene Amplification and Extension, Plant Science, Research and Analysis Methods, Pathology and Laboratory Medicine, Polymerase Chain Reaction, Sphingomonas, Microbiology, Plant and Algal Models, Pseudomonas, Burkina Faso, Medicine and Health Sciences, Grasses, Molecular Biology Techniques, Molecular Biology, Microbial Pathogens, Plant Diseases, Bacteria, Plant Bacterial Pathogens, Coinfection, Plant Anatomy, Incidence, Organisms, Biology and Life Sciences, Eukaryota, Oryza, Plants, Plant Pathology, Bacterial Pathogens, Experimental Organism Systems, Medical Microbiology, Animal Studies, Medicine, Rice, Pathogens, Multiplex Polymerase Chain Reaction, Research Article
Abstract

International audience; Crop diseases are responsible for considerable yield losses worldwide and particularly in sub-Saharan Africa. To implement efficient disease control measures, detection of the pathogens and understanding pathogen spatio-temporal dynamics is crucial and requires the use of molecular detection tools, especially to distinguish different pathogens causing more or less similar symptoms. We report here the design a new molecular diagnostic tool able to simultaneously detect five bacterial taxa causing important diseases on rice in Africa: (1) Pseudomonas fuscovaginae, (2) Xanthomonas oryzae, (3) Burkholderia glumae and Burkholderia gladioli, (4) Sphingomonas and (5) Pantoea species. This new detection tool consists of a multiplex PCR, which is cost effective and easily applicable. Validation of the method is presented through its application on a global collection of bacterial strains. Moreover, sensitivity assessment for the detection of all five bacteria is reported to be at 0.5 ng DNA by μl. As a proof of concept, we applied the new molecular detection method to a set of 256 rice leaves collected from 16 fields in two irrigated areas in western Burkina Faso. Our results show high levels of Sphingomonas spp. (up to 100% of tested samples in one field), with significant variation in the incidence between the two sampled sites. Xanthomonas oryzae incidence levels were mostly congruent with bacterial leaf streak (BLS) and bacterial leaf blight (BLB) symptom observations in the field. Low levels of Pantoea spp. were found while none of the 256 analysed samples was positive for Burkholderia or Pseudomonas fuscovaginae. Finally, many samples (up to 37.5% in one studied field) were positive for more than one bacterium (co-infection). Documenting co-infection levels are important because of their drastic consequences on epidemiology, evolution of pathogen populations and yield losses. The newly designed multiplex PCR for multiple bacterial pathogens of rice is a significant improvement for disease monitoring in the field, thus contributing to efficient disease control and food safety.

Published
2020

70. Additional file of Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

Author

Potnis, Neha, Krasileva, Ksenia, Chow, Virginia, Nalvo F Almeida, Prabhu B Patil, Ryan, Robert P, Sharlach, Molly, Behlau, Franklin, J Max Dow, MT Momol, White, Frank F, Preston, James F, Vinatzer, Boris A, Koebnik, Ralf, Setubal, João C, Norman, David J, Staskawicz, Brian J, and Jones, Jeffrey B

Subjects
fungi, food and beverages, lipids (amino acids, peptides, and proteins), respiratory system, human activities
Abstract

Additional file of Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

Published
2020
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71. The complete genome sequence of Xanthomonas theicola, the causal agent of canker on tea plants, reveals novel secretion systems in clade-1 xanthomonads

Author

Koebnik, Ralf, Burokiene, Daiva, Bragard, Claude, Chang, Christine, Fischer-Le Saux, Marion, Kölliker, Roland, Lang, Jillian, Leach, Jan, Luna, Emily, Portier, Perrine, Sagia, Angeliki, Ziegle, Janet, Cohen, Stephen Philip, Jacobs, Jonathan, UMR - Interactions Plantes Microorganismes Environnement (UMR IPME), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud]), NATURE RESEARCH CENTER VILNIUS LTU, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), INSTITUTE OF LIFE SCIENCES UNIVERSITE CATHOLIQUE DE LOUVAIN LOUVAIN-LA-NEUVE BEL, Pacific Biosciences [Menlo Park], Pacific Biosciences of California, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), DEPARTMENT OF BIOLOGY COLORADO STATE UNIVERSITY FORT COLLINS COLORADO USA, Colorado State University [Fort Collins] (CSU), University of Crete [Heraklion] (UOC), Ohio State University [Columbus] (OSU), United States Department of Agriculture National Institute of Food and Agriculture Postdoctoral Fellowship (2018-08122), for SPC, European Project, UCL - SST/ELI/ELIM - Applied Microbiology, Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ohio State University, and Partenaires INRAE

Subjects
Tea plant, Evolution, pathogen effectors, Plant Science, microbe-genome sequencing, host parasite interactions, Bacterial canker, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Type 3 secretion, bacterial pathogens, Type 2 secretion, genomics, Xanthomonas theicola, Effector-encoding transposon, Agronomy and Crop Science
Abstract

International audience; Xanthomonas theicola is the causal agent of bacterial canker on tea plants. There is no complete genome sequence available for X. theicola, a close relative of the species X. translucens and X. hyacinthi, thus limiting basic research for this group of pathogens. Here we release a highquality complete genome sequence for the X. theicola type strain, CFBP 4691T. Single-molecule real-time sequencing with a mean coverage of 264X revealed two contigs of 4,744,641 bp (chromosome) and 40,955 bp (plasmid) in size. Genome mining revealed the presence of nonribosomal peptide synthases, two CRISPR systems, the Xps type 2 secretion system, and the Hrp type 3 secretion system. Surprisingly, this strain encodes an additional type 2 secretion system and a novel type 3 secretion system with enigmatic function, hitherto undescribed for xanthomonads. Four type 3 effector genes were found on complete or partial transposons, suggesting a role of transposons in effector gene evolution and spread. This genome sequence fills an important gap to better understand the biology and evolution of the early-branching xanthomonads, also known as clade-1 xanthomonads.

Published
2020

72. Additional file 6 of Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

Author

Potnis, Neha, Krasileva, Ksenia, Chow, Virginia, Nalvo F Almeida, Prabhu B Patil, Ryan, Robert P, Sharlach, Molly, Behlau, Franklin, J Max Dow, MT Momol, White, Frank F, Preston, James F, Vinatzer, Boris A, Koebnik, Ralf, Setubal, João C, Norman, David J, Staskawicz, Brian J, and Jones, Jeffrey B

Abstract

Additional file 6:Table S6: Genes/contigs representing T6SS in draft genomes as compared to Xcv. (DOC 44 KB)

Published
2020
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73. Additional file 7 of Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

Author

Potnis, Neha, Krasileva, Ksenia, Chow, Virginia, Nalvo F Almeida, Prabhu B Patil, Ryan, Robert P, Sharlach, Molly, Behlau, Franklin, J Max Dow, MT Momol, White, Frank F, Preston, James F, Vinatzer, Boris A, Koebnik, Ralf, Setubal, João C, Norman, David J, Staskawicz, Brian J, and Jones, Jeffrey B

Abstract

Additional file 7:Table S7: Domain architecture and distribution of proteins with HD-GYP, GGDEF and/or EAL domains encoded by genomes of different Xanthomonas strains. (PDF 348 KB)

Published
2020
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74. Additional file 2 of Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

Author

Potnis, Neha, Krasileva, Ksenia, Chow, Virginia, Nalvo F Almeida, Prabhu B Patil, Ryan, Robert P, Sharlach, Molly, Behlau, Franklin, J Max Dow, MT Momol, White, Frank F, Preston, James F, Vinatzer, Boris A, Koebnik, Ralf, Setubal, João C, Norman, David J, Staskawicz, Brian J, and Jones, Jeffrey B

Abstract

Additional file 2:Figure S2: 1a) Phylogenetic tree based on MUMi indices; 1b) Distance matrix based on MUMi indices. MUMi program was used to calculate pairwise distances between draft genomes and reference Xanthomonas genomes. (PDF 93 KB)

Published
2020
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75. Additional file 8 of Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

Author

Potnis, Neha, Krasileva, Ksenia, Chow, Virginia, Nalvo F Almeida, Prabhu B Patil, Ryan, Robert P, Sharlach, Molly, Behlau, Franklin, J Max Dow, MT Momol, White, Frank F, Preston, James F, Vinatzer, Boris A, Koebnik, Ralf, Setubal, João C, Norman, David J, Staskawicz, Brian J, and Jones, Jeffrey B

Abstract

Additional file 8:Table S8: Genes unique to Xp, grouped in clusters. (DOC 104 KB)

Published
2020
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76. Additional file 3 of Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

Author

Potnis, Neha, Krasileva, Ksenia, Chow, Virginia, Nalvo F Almeida, Prabhu B Patil, Ryan, Robert P, Sharlach, Molly, Behlau, Franklin, J Max Dow, MT Momol, White, Frank F, Preston, James F, Vinatzer, Boris A, Koebnik, Ralf, Setubal, João C, Norman, David J, Staskawicz, Brian J, and Jones, Jeffrey B

Abstract

Additional file 3:Table S3: Whole genome comparisons using MUMmer dnadiff program. % coverage of the aligned contigs and % identities of the respective contigs against reference genomes has been shown for each draft genome. (DOC 36 KB)

Published
2020
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77. Additional file 5 of Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

Author

Potnis, Neha, Krasileva, Ksenia, Chow, Virginia, Nalvo F Almeida, Prabhu B Patil, Ryan, Robert P, Sharlach, Molly, Behlau, Franklin, J Max Dow, MT Momol, White, Frank F, Preston, James F, Vinatzer, Boris A, Koebnik, Ralf, Setubal, João C, Norman, David J, Staskawicz, Brian J, and Jones, Jeffrey B

Abstract

Additional file 5:Table S5: Evidence of the horizontal gene transfer using Alien_hunter analysis. (DOC 33 KB)

Published
2020
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78. Additional file 18 of Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

Author

Potnis, Neha, Krasileva, Ksenia, Chow, Virginia, Nalvo F Almeida, Prabhu B Patil, Ryan, Robert P, Sharlach, Molly, Behlau, Franklin, J Max Dow, MT Momol, White, Frank F, Preston, James F, Vinatzer, Boris A, Koebnik, Ralf, Setubal, João C, Norman, David J, Staskawicz, Brian J, and Jones, Jeffrey B

Subjects
Data_FILES
Abstract

Authors’ original file for figure 8

Published
2020
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80. Additional file 9 of Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

Author

Potnis, Neha, Krasileva, Ksenia, Chow, Virginia, Nalvo F Almeida, Prabhu B Patil, Ryan, Robert P, Sharlach, Molly, Behlau, Franklin, J Max Dow, MT Momol, White, Frank F, Preston, James F, Vinatzer, Boris A, Koebnik, Ralf, Setubal, João C, Norman, David J, Staskawicz, Brian J, and Jones, Jeffrey B

Abstract

Additional file 9:Table S9: Genes common to all pepper pathogens but absent from Xp. (DOC 77 KB)

Published
2020
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81. High-quality genome resource of Xanthomonas hyacinthi generated via long-read sequencing

Author

Cohen, S. P., Luna, E. K., Lang, J. M., Ziegle, J., Chang, C., Leach, J. E., Le-Saux, M. F., Portier, P., Koebnik, Ralf, and Jacobs, J. M.

Subjects
hyacinth, Xanthomonas hyacinthi, food and beverages, SMRT sequencing, yellow disease
Abstract

The bacterial plant pathogen Xanthomonas hyacinthi is the causal agent of yellow disease of Hyacinthus and other ornamental plant genera. There is no available complete genome for X. hyacinthi, limiting basic research for this pathogen. Here, we release a high-quality complete genome sequence for the X. hyacinthi type strain, CFBP 1156. Single-molecule real-time (SMRT) sequencing with a mean coverage of 306x revealed two contigs of 4,918,645 and 44,381 bp in size. This was the first characterized plant-disease-causing species of Xanthomonas and this genome provides a resource to better understand the biology of yellow disease of hyacinth.

Published
2020

82. Genome resources of three west African strains of Pantoea ananatis causing bacterial blight and grain discoloration of rice

Author

Kini, Kossi, Lefeuvre, Pierre, Poulin, Lucie, Silué, Drissa, Koebnik, Ralf, Kini, Kossi, Lefeuvre, Pierre, Poulin, Lucie, Silué, Drissa, and Koebnik, Ralf

Abstract

Members of the genus Pantoea have been reported as pathogens for many economically important crops, including rice. Little is known about their host−pathogen interactions at the molecular level and the lack of comprehensive genome data impedes targeted breeding strategies toward resistant rice cultivars. Here, we describe the structural and functional annotation of the draft genome sequences of three rice-pathogenic Pantoea ananatis strains, ARC272, ARC310, and ARC311, which were isolated in Burkina Faso, Togo, and Benin, respectively. The genome sequences of these strains will help in developing molecular diagnostic tools and provide new insight into common traits that may enable P. ananatis to infect rice.

Published
2020

83. Repeated gain and loss of a single gene modulates the evolution of vascular plant pathogen lifestyles

Author

UCL - SST/ELI/ELIM - Applied Microbiology, Gluck-Thaler, Emile, Cerutti, Aude, Perez-Quintero, Alvaro L., Butchacas, Jules, Roman-Reyna, Verónica, Madhavan, Vishnu Narayanan, Shantharaj, Deepak, Merfa, Marcus V., Pesce, Céline, Jauneau, Alain, Vancheva, Taca, Lang, Jillian M., Allen, Caitilyn, Verdier, Valerie, Gagnevin, Lionel, Szurek, Boris, Beckham, Gregg T., De La Fuente, Leonardo, Patel, Hitendra Kumar, Sonti, Ramesh V., Bragard, Claude, Leach, Jan E., Noël, Laurent D., Slot, Jason C., Koebnik, Ralf, Jacobs, Jonathan M., UCL - SST/ELI/ELIM - Applied Microbiology, Gluck-Thaler, Emile, Cerutti, Aude, Perez-Quintero, Alvaro L., Butchacas, Jules, Roman-Reyna, Verónica, Madhavan, Vishnu Narayanan, Shantharaj, Deepak, Merfa, Marcus V., Pesce, Céline, Jauneau, Alain, Vancheva, Taca, Lang, Jillian M., Allen, Caitilyn, Verdier, Valerie, Gagnevin, Lionel, Szurek, Boris, Beckham, Gregg T., De La Fuente, Leonardo, Patel, Hitendra Kumar, Sonti, Ramesh V., Bragard, Claude, Leach, Jan E., Noël, Laurent D., Slot, Jason C., Koebnik, Ralf, and Jacobs, Jonathan M.

Abstract

Vascular plant pathogens travel long distances through host veins, leading to life-threatening, systemic infections. In contrast, nonvascular pathogens remain restricted to infection sites, triggering localized symptom development. The contrasting features of vascular and nonvascular diseases suggest distinct etiologies, but the basis for each remains unclear. Here, we show that the hydrolase CbsA acts as a phenotypic switch between vascular and nonvascular plant pathogenesis. cbsA was enriched in genomes of vascular phytopathogenic bacteria in the family Xanthomonadaceae and absent in most nonvascular species. CbsA expression allowed nonvascular Xanthomonas to cause vascular blight, while cbsA mutagenesis resulted in reduction of vascular or enhanced nonvascular symptom development. Phylogenetic hypothesis testing further revealed that cbsA was lost in multiple nonvascular lineages and more recently gained by some vascular subgroups, suggesting that vascular pathogenesis is ancestral. Our results overall demonstrate how the gain and loss of single loci can facilitate the evolution of complex ecological traits.

Published
2020

84. Repeated gain and loss of a single gene modulates the evolution of vascular plant pathogen lifestyles

Author

Gluck-Thaler, E., Cerutti, Aude, Pérez-Quintero, Alvaro L., Butchacas, Jules, Roman-Reyna, Verónica, Madhavan, Vishnu Narayanan, Shantharaj, Deepak, Merfa, Marcus V., Pesce, Céline, Jauneau, Alain, Vancheva, T., Lang, Jillian M., Allen, Caitilyn, Verdier, Valérie, Gagnevin, Lionel, Szurek, Boris, Beckham, Gregg T., De La Fuente, Leonardo, Patel, Hitendra Kumar, Sonti, Ramesh V., Bragard, Claude, Leach, Jan E., Noel, Laurent D., Slot, J., Koebnik, Ralf, Jacobs, Jonathan M., Gluck-Thaler, E., Cerutti, Aude, Pérez-Quintero, Alvaro L., Butchacas, Jules, Roman-Reyna, Verónica, Madhavan, Vishnu Narayanan, Shantharaj, Deepak, Merfa, Marcus V., Pesce, Céline, Jauneau, Alain, Vancheva, T., Lang, Jillian M., Allen, Caitilyn, Verdier, Valérie, Gagnevin, Lionel, Szurek, Boris, Beckham, Gregg T., De La Fuente, Leonardo, Patel, Hitendra Kumar, Sonti, Ramesh V., Bragard, Claude, Leach, Jan E., Noel, Laurent D., Slot, J., Koebnik, Ralf, and Jacobs, Jonathan M.

Abstract

Vascular plant pathogens travel long distances through host veins, leading to life-threatening, systemic infections. In contrast, nonvascular pathogens remain restricted to infection sites, triggering localized symptom development. The contrasting features of vascular and nonvascular diseases suggest distinct etiologies, but the basis for each remains unclear. Here, we show that the hydrolase CbsA acts as a phenotypic switch between vascular and nonvascular plant pathogenesis. cbsA was enriched in genomes of vascular phytopathogenic bacteria in the family Xanthomonadaceae and absent in most nonvascular species. CbsA expression allowed nonvascular Xanthomonas to cause vascular blight, while cbsA mutagenesis resulted in reduction of vascular or enhanced nonvascular symptom development. Phylogenetic hypothesis testing further revealed that cbsA was lost in multiple nonvascular lineages and more recently gained by some vascular subgroups, suggesting that vascular pathogenesis is ancestral. Our results overall demonstrate how the gain and loss of single loci can facilitate the evolution of complex ecological traits. evolution of complex ecological traits.

Published
2020

85. Specific binding of the Xanthomonas campestris pv. vesicatoria AraC-type transcriptional activator HrpX to plant-inducible promoter boxes

Author

Koebnik, Ralf, Kruger, Antje, Thieme, Frank, Urban, Alexander, and Bonas, Ulla

Subjects
Nucleotide sequence -- Research, Gene expression -- Research, Hydrolases -- Research, Enzymes -- Research, Biological sciences
Abstract

The pathogenicity of the plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria depends on a type III secretion system which is encoded by the 23-kb hrp (hypersensitive response and pathogenicity) gene cluster. Expression of the hrp operons is strongly induced in planta and in a special minimal medium and depends on two regulatory proteins, HrpG and HrpX. In this study, DNA affinity enrichment was used to demonstrate that the AraC-type transcriptional activator HrpX binds to a conserved cis-regulatory element, the plant-inducible promoter (PIP) box (TTCGC-[N.sub.15]-TTCGC), present in the promoter regions of four hrp operons. No binding of HrpX was observed when DNA fragments lacking a PIP box were used. HrpX also bound to a DNA fragment containing an imperfect PIP box (TTCGC-[N.sub.8]-TTCGT). Dinucleotide replacements in each half-site of the PIP box strongly decreased binding of HrpX, while simultaneous dinucleotide replacements in both half-sites completely abolished binding. Based on the complete genome sequence of Xanthomonas campestris pv. vesicatoria, putative plant-inducible promoters consisting of a PIP box and a -10 promoter motif were identified in the promoter regions of almost all HrpX-activated genes. Bioinformatic analyses and reverse transcription-PCR experiments revealed novel HrpX-dependent genes, among them a NUDIX hydrolase gene and several genes with a predicted role in the degradation of the plant cell wall. We conclude that HrpX is the most downstream component of the hrp regulatory cascade, which is proposed to directly activate most genes of the hrpX regulon via binding to corresponding PIP boxes.

Published
2006

86. Positive selection of the Hrp pilin HrpE of the plant pathogen Xanthomonas

Author

Weber, Ernst and Koebnik, Ralf

Subjects
Bacteria, Pathogenic -- Genetic aspects, Bacteria, Pathogenic -- Structure, Nucleotide sequence -- Research, Plant defenses -- Research, Polymerization -- Analysis, Biological sciences
Abstract

The plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria possesses a type III secretion (TTS) system which is encoded by the 23-kb hrp (hypersensitive response and pathogenicity) gene cluster. The TTS system is necessary for pathogenicity in susceptible hosts and induction of the hypersensitive response in resistant plants. At the cell surface, the TTS system is associated with an extracellular filamentous structure, the Hrp pilus, which serves as a conduit for the transfer of bacterial proteins into the plant cell cytosol. The major pilus component, the HrpE pilin, is unique to xanthomonads. Previous work showed that HrpE contains two regions: a hypervariable surface-exposed domain, including the N-terminal secretion signal, and a C-terminal polymerization domain. In this study, the evolutionary rate of the hrpE gene was analyzed. Twenty-one alleles were cloned, sequenced, and compared with five known hrpE alleles. The ratio of synonymous ([K.sub.s]) and nonsynonymous ([K.sub.a]) substitution rates shows that parts of the HrpE N terminus are subjected to positive selection and the C terminus is subjected to purifying selection. The trade-off between positive and purifying selection at the very-N terminus allowed us to ascertain the amphipathic [alpha]-helical nature of the TTS signal. This is the first report of a surface structure from a plant-pathogenic bacterium that evolved under the constraint of positive selection and hints to the evolutionary adaptation of this extracellular appendage to avoid recognition by the plant defense surveillance system.

Published
2006

88. Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence

Author

Thieme, Frank, Koebnik, Ralf, Bekel, Thomas, Berger, Carolin, Boch, Jens, Buttner, Daniela, Caldana, Camila, Gaigalat, Lars, Goesmann, Alexander, Kay, Sabine, Kirchner, Oliver, Lanz, Christa, Linke, Burkhard, McHardy, Alice C., Meyer, Folker, Mittenhuber, Gerhard, Nies, Dietrich H., Niesbach-Klosgen, Ulla, Patschkowski, Thomas, Ruckert, Christian, Rupp, Oliver, Schneiker, Susanne, Schuster, Stephan C., Vorholter, Frank-Jorg, Weber, Ernst, Puhler, Alfred, Bonas, Ulla, Bartels, Daniela, and Kaiser, Olaf

Subjects
Nucleotide sequence -- Research, Microbial polysaccharides -- Research, Bacterial proteins -- Research, Genetic research, Biological sciences
Abstract

The gram-negative plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria is the causative agent of bacterial spot disease in pepper and tomato plants, which leads to economically important yield losses. This pathosystem has become a well-established model for studying bacterial infection strategies. Here, we present the whole-genome sequence of the pepper-pathogenic Xanthomonas campestris pv. vesicatoria strain 85-10, which comprises a 5.17-Mb circular chromosome and four plasmids. The genome has a high G+C content (64.75%) and signatures of extensive genome plasticity. Whole-genome comparisons revealed a gene order similar to both Xanthomonas axonopodis pv. citri and Xanthomonas campestris pv. campestris and a structure completely different from Xanthomonas oryzae pv. oryzae. A total of 548 coding sequences (12.2%) are unique to X. campestris pv. vesicatoria. In addition to a type III secretion system, which is essential for pathogenicity., the genome of strain 85-10 encodes all other types of protein secretion systems described so far in gram-negative bacteria. Remarkably, one of the putative type IV secretion systems encoded on the largest plasmid is similar to the Icm/Dot systems of the human pathogens Legionella pneumophila and Coxiella burnetii. Comparisons with other completely sequenced plant pathogens predicted six novel type III effector proteins and several other virulence factors, including adhesins, cell wall-degrading enzymes, and extracellular polysaccharides.

Published
2005

89. Domain structure of HrpE, the Hrp pilus subunit of Xanthomonas campestris pv. vesicatoria

Author

Weber, Ernst and Koebnik, Ralf

Subjects
Xanthoma -- Research, Genetic research, Biological sciences
Abstract

The plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria possesses a type III secretion (TTS) system necessary for pathogenicity in susceptible hosts and induction of the hypersensitive response in resistant plants. This specialized protein transport system is encoded by a 23-kb hrp (hypersensitive response and pathogenicity) gene cluster. X. campestris pv. vesicatoria produces filamentous structures, Hrp pili, at the cell surface under hrp-inducing conditions. The Hrp pilus acts as a cell surface appendage of the TTS system and serves as a conduit for the transfer of bacterial effector proteins into the plant cell cytosol. The major pilus component, the HrpE pilin, is unique to xanthomonads and is encoded within the hrp gene cluster. In this study, functional domains of HrpE were mapped by linker-scanning mutagenesis and by reporter protein fusions to an N-terminally truncated avirulence protein (AvrBs3A2). Thirteen five-amino-acid peptide insertion mutants were obtained and could be grouped into six phenotypic classes. Three permissive mutations were mapped in the N-terminal half of HrpE, which is weakly conserved within the HrpE protein family. Four dominant-negative peptide insertions in the strongly conserved C-terminal region suggest that this domain is critical for oligomerization of the pilus subunits. Reporter protein fusions revealed that the N-terminal 17 amino acid residues act as an efficient TTS signal. From these results, we postulate a three-domain structure of HrpE with an N-terminal secretion signal, a surface-exposed variable region of the N-terminal half, and a C-terminal polymerization domain. Comparisons with a mutant study of HrpA, the Hrp pilin from Pseudomonas syringae pv. tomato DC3000, and hydrophobicity plot analyses of several nonhomologous Hrp pilins suggest a common architecture of Hrp pilins of different plant-pathogenic bacteria.

Published
2005

90. Repeated gain and loss of a single gene modulates the evolution of vascular plant pathogen lifestyles

Author

Gluck-Thaler, Emile, primary, Cerutti, Aude, additional, Perez-Quintero, Alvaro L., additional, Butchacas, Jules, additional, Roman-Reyna, Verónica, additional, Madhavan, Vishnu Narayanan, additional, Shantharaj, Deepak, additional, Merfa, Marcus V., additional, Pesce, Céline, additional, Jauneau, Alain, additional, Vancheva, Taca, additional, Lang, Jillian M., additional, Allen, Caitilyn, additional, Verdier, Valerie, additional, Gagnevin, Lionel, additional, Szurek, Boris, additional, Beckham, Gregg T., additional, De La Fuente, Leonardo, additional, Patel, Hitendra Kumar, additional, Sonti, Ramesh V., additional, Bragard, Claude, additional, Leach, Jan E., additional, Noël, Laurent D., additional, Slot, Jason C., additional, Koebnik, Ralf, additional, and Jacobs, Jonathan M., additional

Published
2020
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91. The type III-dependent Hrp pilus is required for productive interaction of Xanthomonas campestris pv. vesicatoria with pepper host plants

Author

Weber, Ernst, Ojanen-Reuhs, Tuula, Huguet, Elisabeth, Hause, Gerd, Romantschuk, Martin, Korhonen, Timo K., Bonas, Ulla, and Koebnik, Ralf

Subjects
Bacteriology -- Research, Bacteria, Pathogenic -- Research, Biological sciences
Abstract

The plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria expresses a type III secretion system that is necessary for both pathogenicity in susceptible hosts and the induction of the hypersensitive response in resistant plants. This specialized protein transport system is encoded by a 23-kb hrp (hypersensitive response and pathogenicity) gene cluster. Here we show that X. campestris pv. vesicatoria produces filamentous structures, the Hrp pili, at the cell surface under hrp-inducing conditions. Analysis of purified Hrp pili and immunoelectron microscopy revealed that the major component of the Hrp pilus is the HrpE protein which is encoded in the hrp gene cluster. Sequence homologues of hrpE are only found in other xanthomonads. However, hrpE is syntenic to the hrpY gene from another plant pathogen, Ralstonia solanacearum. Bioinformatic analyses suggest that all major Hrp pilus subunits from gram-negative plant pathogens may share the same structural organization, i.e., a predominant alpha-helical structure. Analysis of nonpolar mutants in hrpE demonstrated that the Hrp pilus is essential for the productive interaction of X. campestris pv. vesicatoria with pepper host plants. Furthermore, a functional Hrp pilus is required for type III-dependent protein secretion. Immunoelectron microscopy revealed that type III-secreted proteins, such as HrpF and AvrBs3, are in close contact with the Hrp pilus during and/or after their secretion. By systematic analysis of nonpolar hrp/hrc (hrp conserved) and hpa (hrp associated) mutants, we found that Hpa proteins as well as the translocon protein HrpF are dispensable for pilus assembly, while all other Hrp and Hrc proteins are required. Hence, there are no other conserved Hrp or Hrc proteins that act downstream of HrpE during type III-dependent protein translocation.

Published
2005

93. Repeated gain and loss of a single gene modulates the evolution of vascular pathogen lifestyles

Author

Gluck-Thaler, Emile, primary, Cerutti, Aude, additional, Perez-Quintero, Alvaro, additional, Butchacas, Jules, additional, Roman-Reyna, Verónica, additional, Madhaven, Vishnu Narayanan, additional, Shantharaj, Deepak, additional, Merfa, Marcus V., additional, Pesce, Céline, additional, Jauneau, Alain, additional, Vancheva, Taca, additional, Lang, Jillian M., additional, Allen, Caitilyn, additional, Verdier, Valerie, additional, Gagnevin, Lionel, additional, Szurek, Boris, additional, Cunnac, Sébastien, additional, Beckham, Gregg, additional, de la Fuente, Leonardo, additional, Patel, Hitendra Kumar, additional, Sonti, Ramesh V, additional, Bragard, Claude, additional, Leach, Jan E., additional, Noël, Laurent D., additional, Slot, Jason C., additional, Koebnik, Ralf, additional, and Jacobs, Jonathan M., additional

Published
2020
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97. Structural and functional roles of the surface-exposed loops of the b-barrel membrane protein OmpA from Escherichia coli

Author

Koebnik, Ralf

Subjects
Escherichia coli -- Physiological aspects, Membrane proteins -- Research, Cell membranes -- Formation, Biological sciences
Abstract

The B-barrel protein OmpA of Escherichia coli plays a significant role in maintaining the stability of mating aggregates in an F conjugation. By decreasing the length of the transmembrane B-strands of the strain in all possible ways, it was also found that the protein functions as a primary component of the B-structured integral membrane. However, the existence of topogenic signals including charge distribution and loop charges in these strains was negated.

Published
1999

99. Transmembrane signaling across the ligand-gated FhuA receptor: crystal structures of free and ferrichrome-bound states reveal allosteric changes

Author

Locher, Kaspar P., Rees, Bernard, Koebnik, Ralf, Mitschler, Andre, Moulinier, Luc, Rosenbusch, Jurg P., and Moras, Dino

Subjects
Membrane proteins -- Research, Ligand binding (Biochemistry) -- Research, Iron compounds -- Research, Bacterial cell walls -- Research, Cellular signal transduction -- Research, Biological sciences
Abstract

A study was undertaken to determine the role of the ferric hydroxymate uptake protein component A (FhuA) in facilitating the ligand-gated transport of the siderophore ferrichrome. The structure of the protein revealed two domains and the binding site of the ferrichrome was at the apical interface of three turns of the plug domain and two loops of the barrel. The ferrichrome binding activated the interactions of the energy transducing TonB complex with the periplasmic surface of the FhuA protein.

Published
1998

100. MOESM12 of CRISPR elements provide a new framework for the genealogy of the citrus canker pathogen Xanthomonas citri pv. citri

Author

Kwanho Jeong, Muñoz-Bodnar, Alejandra, Rojas, Nathalia Arias, Poulin, Lucie, Rodriguez-R, Luis, Gagnevin, Lionel, Vernière, Christian, Pruvost, Olivier, and Koebnik, Ralf

Abstract

Additional file 12: Figure S9. Primer design for PCR amplification of CRISPR regions adjacent to an IS element. A, primer combinations used for strains LB302, LB305, LG115 and NCPPB 3608; B, primer combinations used for strain LG097. Forward primers are shown as red rectangles with an arrow, reverse primers are represented by blue rectangles with an arrow. The yellow triangle indicates the leader sequence and the red triangle indicates the terminator sequence. Deep blue rectangles indicate CRISPR repeats. CRISPR spacers are represented by green diamonds. Spacers are numbered from 1 to 23, starting with the terminator proximal spacer, which presumably represents the oldest spacer. Orange rectangles indicate IS elements.

Published
2019
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